[2024-01-24 13:55:43,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:43,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:43,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference
[2024-01-24 13:55:45,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:45,094] [INFO] Task started: Prodigal
[2024-01-24 13:55:45,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg5555d248-a4d1-4080-9c37-8a38ec731615/GCF_022557235.1_ASM2255723v1_genomic.fna.gz | prodigal -d GCF_022557235.1_ASM2255723v1_genomic.fna/cds.fna -a GCF_022557235.1_ASM2255723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:09,041] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:09,041] [INFO] Task started: HMMsearch
[2024-01-24 13:56:09,041] [INFO] Running command: hmmsearch --tblout GCF_022557235.1_ASM2255723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/reference_markers.hmm GCF_022557235.1_ASM2255723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:09,423] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:09,424] [INFO] Found 6/6 markers.
[2024-01-24 13:56:09,473] [INFO] Query marker FASTA was written to GCF_022557235.1_ASM2255723v1_genomic.fna/markers.fasta
[2024-01-24 13:56:09,474] [INFO] Task started: Blastn
[2024-01-24 13:56:09,474] [INFO] Running command: blastn -query GCF_022557235.1_ASM2255723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/reference_markers.fasta -out GCF_022557235.1_ASM2255723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:10,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:10,444] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:10,445] [INFO] Target genome list was writen to GCF_022557235.1_ASM2255723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:10,456] [INFO] Task started: fastANI
[2024-01-24 13:56:10,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg5555d248-a4d1-4080-9c37-8a38ec731615/GCF_022557235.1_ASM2255723v1_genomic.fna.gz --refList GCF_022557235.1_ASM2255723v1_genomic.fna/target_genomes.txt --output GCF_022557235.1_ASM2255723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:23,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:23,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:23,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:23,117] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {317: 'Pseudomonas syringae', 251699: 'Pseudomonas syringae group genomosp. 7', 251701: 'Pseudomonas syringae group genomosp. 3'}, {}
[2024-01-24 13:56:23,118] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:56:23,118] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:56:23,118] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	100.0	2103	2109	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4531	GCA_001400835.1	251699	251699	type	True	99.9324	1929	2109	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_001401315.1	251699	251699	pathovar	True	98.9879	1820	2109	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	98.9734	1912	2109	95	inconclusive
Pseudomonas caricapapayae	strain=CCUG 32775T	GCA_008692855.1	46678	46678	type	True	97.5469	1815	2109	95	inconclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	89.5032	1645	2109	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	79.4717	729	2109	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	79.4378	722	2109	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:23,120] [INFO] DFAST Taxonomy check result was written to GCF_022557235.1_ASM2255723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:23,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:23,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:23,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/checkm_data
[2024-01-24 13:56:23,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:23,179] [INFO] Task started: CheckM
[2024-01-24 13:56:23,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022557235.1_ASM2255723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022557235.1_ASM2255723v1_genomic.fna/checkm_input GCF_022557235.1_ASM2255723v1_genomic.fna/checkm_result
[2024-01-24 13:57:32,724] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:32,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:32,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:32,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:32,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022557235.1_ASM2255723v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:32,750] [INFO] Task started: Blastn
[2024-01-24 13:57:32,750] [INFO] Running command: blastn -query GCF_022557235.1_ASM2255723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6399052c-994a-4352-834e-76fe9ad9eea0/dqc_reference/reference_markers_gtdb.fasta -out GCF_022557235.1_ASM2255723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:34,283] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:34,287] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:34,287] [INFO] Target genome list was writen to GCF_022557235.1_ASM2255723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:34,342] [INFO] Task started: fastANI
[2024-01-24 13:57:34,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg5555d248-a4d1-4080-9c37-8a38ec731615/GCF_022557235.1_ASM2255723v1_genomic.fna.gz --refList GCF_022557235.1_ASM2255723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022557235.1_ASM2255723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:52,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,700] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:52,700] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001400735.1	s__Pseudomonas_E caricapapayae	97.4443	1768	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	conclusive
GCF_002699855.1	s__Pseudomonas_E amygdali	89.4368	1549	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	-
GCF_900074915.1	s__Pseudomonas_E cerasi	88.6919	1678	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.51	98.33	0.88	0.83	51	-
GCF_009176725.1	s__Pseudomonas_E syringae_M	88.6447	1586	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	98.71	98.38	0.92	0.88	59	-
GCF_900103225.1	s__Pseudomonas_E congelans	88.61	1623	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_000507185.2	s__Pseudomonas_E syringae	88.3301	1610	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	-
GCF_000444135.1	s__Pseudomonas_E avellanae	87.0908	1454	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	85.6887	1496	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	85.6302	1499	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_900108875.1	s__Pseudomonas_E sp900108875	80.513	915	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019445.1	s__Pseudomonas_E putida_E	79.673	682	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	78.8815	640	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,702] [INFO] GTDB search result was written to GCF_022557235.1_ASM2255723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:52,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:52,708] [INFO] DFAST_QC result json was written to GCF_022557235.1_ASM2255723v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:52,709] [INFO] DFAST_QC completed!
[2024-01-24 13:57:52,709] [INFO] Total running time: 0h2m9s